Quarterly Taxes Explained for LLCs with S‑Corp Election: Do You Need to Pay & How to Calculate

If you’ve elected S‑Corp status for your Single‑Member LLC, congrats—you’re optimizing your taxes. But that also means quarterly tax payments are a critical part of your strategy, especially with tax season around the corner.

While your payroll covers part of it, you're still responsible for quarterly estimated taxes on your K‑1 income—and missing payments can trigger IRS penalties.

Here’s how to handle it the smart way.

🔍 Why S‑Corp LLC Owners Still Pay Quarterly Taxes

✅ As an S‑Corp owner, the business files Form 1120‑S and issues you a Schedule K‑1 for your share of profits. (H&R Block Tax preparation company, WCG CPAs & Advisors)
✅ You pay yourself a reasonable salary through payroll, with taxes withheld through each paycheck. Your business covers half, and you cover half of FICA taxes. (Wikipedia, WCG CPAs & Advisors)
✅ However, any pass‑through income beyond your salary is still taxable—and must be covered via quarterly estimated taxes. The IRS expects you to prepay income tax on this extra K‑1 income. (Collective)

💡 How to Calculate Quarterly Estimated Taxes for Your S‑Corp LLC

1. Project your annual K‑1 income, excluding your salary.

2. Estimate tax liability: Combine your marginal tax rate and self-tax exposure on that K‑1 income.

3. Account for withholdings from payroll (W‑2 withholding).

4. Use IRS safe harbor rules (paying at least 100% of last year’s tax or 90% of current-year liability) to avoid penalties. (WCG CPAs & Advisors, The Wall Street Journal)

5. Divide the remaining tax due into four equal payments—due April 15, June 15, September 15, and January 15. (Collective)

📆 Why Payroll Alone Isn’t Enough

Payroll withholding covers your salary—not your business profits via K‑1. Failing to make quarterly payments on that K‑1 income can result in penalties—even if you're current on payroll taxes. (WCG CPAs & Advisors)

One accountant shared:

“You are essentially making estimated tax payments in two ways… through payroll taxes … and through payments made by you personally.” (WCG CPAs & Advisors)

❓ FAQ: S‑Corp Estimated Taxes for LLC Owners

Q: Do I pay quarterly taxes on my salary?
A: No, payroll withholding covers that—but you still owe estimated tax on distributed K‑1 income.

Q: What if I underpay or miss deadlines?
A: The IRS charges penalties and interest—especially with today’s high underpayment rate.   (The Wall Street Journal, IRS)

Q: Can I skip estimated payments if I withheld extra on payroll?
A: Possibly. If your payroll withholding covers 100% of last year’s tax or 90% of this year’s liability, you may avoid penalties. (IRS)

💡 “With S‑Corp LLCs, you're running payroll—and paying taxes on profits. Missing one piece leaves your tax strategy incomplete.”
Dr. Bryan Raya helps S‑Corp owners fine-tune their tax withholding and estimated payment strategy for clarity and compliance.

📞 Schedule your free call with Dr. Raya today to map out your estimated tax plan—and start Doing Business Right.

🔖 #selfemployedtaxes #estimatedtaxes #LLCSCorp #quarterlypayments #dbrbookkeeping #quickbooksadvisor #taxplanning #doingbusinessright